PROJECT SUMMARY Autism spectrum disorders (ASDs) affect 1% of the general population, and epilepsy (EPI) is observed in at least one-third of ASD individuals. ASDs with epilepsy (ASD-EPI) are typically more severe and treatment delay has a negative impact on outcome. The frequent association between epileptic and autistic phenotypes suggests that they share predisposing genes. Indeed, in recent years it has become clear that genes implicated in ASD and EPI, as well as other neurodevelopmental disorders, are interconnected in functional networks. Strikingly, there is a considerable overlap in the networks affected in each disorder, raising questions on how disruptions of these common networks can give rise to such phenotypical diversity. Despite ongoing large-scale efforts to identify risk genes for ASD, and to a lesser extent for pediatric EPI, the diagnostic yield remains low and most causal genes and risk variants are yet to be identified. New cohorts are also needed to discover additional variants in previously identified candidate genes and elevate them to the status of ASD-EPI risk genes. Our study differs from previous efforts by focusing on a set of 550 families with a specific ASD-EPI sub-phenotype that will result in less phenotypic heterogeneity to increase power to find variants in this specific subtype. For each family we will sequence the complete exome, as well as noncoding regulatory regions near genes with strong prior evidence for association with ASD and/or EPI. We will perform burden analysis of rare de novo and inherited gene-disruptive events in ASD-EPI, and correlate with clinical phenotype variables (early vs late-onset epilepsy, gender, IQ, and MRI abnormalities), and incorporate this into existing ASD/EPI datasets for gene-set and network analyses, as well as integrating SNVs and CNVs in a common framework (Aim 1). We will also identify risk variants in noncoding regulatory elements, including cis- regulatory elements near implicated, high confidence, and/or candidate genes for ASD and EPI (ASD/EPI- relevant genes), intronic RBFOX binding targets, and miRNA binding targets, using a new statistical framework followed by burden analyses (Aim 2). Finally, we will functionally characterize 8 high-impact variants, which will be introduced by CRISPR genome editing into isogenic human induced pluripotent stem cells (iPSCs) and further differentiated into forebrain neuronal progenitor cells (NPCs) and neurons. Functional assays will include RNA-Seq, neuronal connectivity and morphology, as well as activity using Multi-Electrode Arrays (Aim 3). The identification and functional characterization of additional mutations will help prioritize genes and reveal novel components of the pathways underlying ASD-EPI, and provide mechanistic insight into how they relate to each other. Our systematic approach also provides the opportunity to classify molecular subtypes of ASD/EPI and to distinguish how the genetic subnetworks underlying ASD-EPI differ from the framework of pathways associated with each disorder, as necessary steps toward tailored intervention and treatment. Our proposal will set a standard for rapid and large-scale screening for ASD and related neurodevelopmental disorders.